--- /dev/null
+\hypertarget{part__func_8h}{\section{part\-\_\-func.\-h}
+\label{part__func_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.\-h}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_}
+00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_}
+00003 \textcolor{preprocessor}{}
+00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
+00005
+00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
+00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
+00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
+00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
+00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00011 \textcolor{preprocessor}{}
+00012
+00041 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\_back};
+00042
+00043 \textcolor{comment}{/*}
+00044 \textcolor{comment}{#################################################}
+00045 \textcolor{comment}{# PARTITION FUNCTION COMPUTATION #}
+00046 \textcolor{comment}{#################################################}
+00047 \textcolor{comment}{*/}
+00048
+00087 \textcolor{keywordtype}{float} \hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\_fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
+00088 \textcolor{keywordtype}{char} *structure,
+00089 \hyperlink{structpf__paramT}{pf\_paramT} *parameters,
+00090 \textcolor{keywordtype}{int} calculate\_bppm,
+00091 \textcolor{keywordtype}{int} is\_constrained,
+00092 \textcolor{keywordtype}{int} is\_circular);
+00093
+00133 \textcolor{keywordtype}{float} \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
+00134 \textcolor{keywordtype}{char} *structure);
+00135
+00161 \textcolor{keywordtype}{float} \hyperlink{group__pf__fold_ga819ce5fca8984004ac81c4a3b04cb735}{pf\_circ\_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
+00162 \textcolor{keywordtype}{char} *structure);
+00163
+00173 \textcolor{keywordtype}{char} *\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack}(\textcolor{keywordtype}{char} *sequence);
+00174
+00186 \textcolor{keywordtype}{char} *\hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_circ}(\textcolor{keywordtype}{char} *sequence);
+00187
+00203 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}(\textcolor{keywordtype}{void});
+00204
+00214 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\_pf\_params}(\textcolor{keywordtype}{int} length);
+00215
+00222 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{update\_pf\_params\_par}(\textcolor{keywordtype}{int} length, \hyperlink{structpf__paramT}{pf\_paramT} *parameters);
+00223
+00240 FLT\_OR\_DBL *\hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(\textcolor{keywordtype}{void});
+00241
+00242 \textcolor{comment}{/*}
+00243 \textcolor{comment}{#################################################}
+00244 \textcolor{comment}{# OTHER PARTITION FUNCTION RELATED DECLARATIONS #}
+00245 \textcolor{comment}{#################################################}
+00246 \textcolor{comment}{*/}
+00247
+00265 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\_plist\_from\_pr}( \hyperlink{structplist}{plist} **pl,
+00266 FLT\_OR\_DBL *probs,
+00267 \textcolor{keywordtype}{int} length,
+00268 \textcolor{keywordtype}{double} cutoff);
+00269
+00270 \textcolor{comment}{/* this doesn't work if free\_pf\_arrays() is called before */}
+00271 \textcolor{keywordtype}{void} assign\_plist\_gquad\_from\_pr(\hyperlink{structplist}{plist} **pl,
+00272 \textcolor{keywordtype}{int} length,
+00273 \textcolor{keywordtype}{double} cut\_off);
+00274
+00275 \textcolor{keywordtype}{char} *get\_centroid\_struct\_gquad\_pr(\textcolor{keywordtype}{int} length,
+00276 \textcolor{keywordtype}{double} *dist);
+00277
+00293 \textcolor{keywordtype}{int} \hyperlink{group__pf__fold_ga18607e79e106cad827f482eedd2f632e}{get\_pf\_arrays}(\textcolor{keywordtype}{short} **S\_p,
+00294 \textcolor{keywordtype}{short} **S1\_p,
+00295 \textcolor{keywordtype}{char} **ptype\_p,
+00296 FLT\_OR\_DBL **qb\_p,
+00297 FLT\_OR\_DBL **qm\_p,
+00298 FLT\_OR\_DBL **q1k\_p,
+00299 FLT\_OR\_DBL **qln\_p);
+00300
+00304 \textcolor{keywordtype}{double} \hyperlink{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{get\_subseq\_F}(\textcolor{keywordtype}{int} i, \textcolor{keywordtype}{int} j);
+00305
+00322 \textcolor{keywordtype}{char} *\hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\_centroid\_struct\_pl}(\textcolor{keywordtype}{int} length,
+00323 \textcolor{keywordtype}{double} *dist,
+00324 \hyperlink{structplist}{plist} *pl);
+00325
+00342 \textcolor{keywordtype}{char} *\hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\_centroid\_struct\_pr}(\textcolor{keywordtype}{int} length,
+00343 \textcolor{keywordtype}{double} *dist,
+00344 FLT\_OR\_DBL *pr);
+00345
+00358 \textcolor{keywordtype}{double} \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\_bp\_distance}(\textcolor{keywordtype}{int} length);
+00359
+00377 \textcolor{keywordtype}{double} \hyperlink{group__pf__fold_ga72d84525f0afd3a9d60d830a2f501fa5}{mean\_bp\_distance\_pr}(\textcolor{keywordtype}{int} length,
+00378 FLT\_OR\_DBL *pr);
+00379
+00383 \textcolor{keywordtype}{void} \hyperlink{part__func_8h_a1f562d463c14d4703d9656056200eb38}{bppm\_to\_structure}(\textcolor{keywordtype}{char} *structure,
+00384 FLT\_OR\_DBL *pr,
+00385 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
+00386
+00387 \hyperlink{structplist}{plist} *stackProb(\textcolor{keywordtype}{double} cutoff);
+00388
+00392 \textcolor{keywordtype}{char} \hyperlink{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{bppm\_symbol}(\textcolor{keyword}{const} \textcolor{keywordtype}{float} *x);
+00393
+00394
+00395 \textcolor{comment}{/*}
+00396 \textcolor{comment}{#################################################}
+00397 \textcolor{comment}{# DEPRECATED FUNCTIONS #}
+00398 \textcolor{comment}{#################################################}
+00399 \textcolor{comment}{*/}
+00400
+00406 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\_pf\_fold}(\textcolor{keywordtype}{int} length));
+00407
+00412 DEPRECATED(\textcolor{keywordtype}{char} *\hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid}(\textcolor{keywordtype}{int} length,
+00413 \textcolor{keywordtype}{double} *dist)); \textcolor{comment}{/* mean pair distance of ensemble */}
+00414
+00420 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\_bp\_dist}(\textcolor{keywordtype}{int} length));
+00421
+00425 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy}(\textcolor{keywordtype}{int} u1,
+00426 \textcolor{keywordtype}{int} u2,
+00427 \textcolor{keywordtype}{int} type,
+00428 \textcolor{keywordtype}{int} type2,
+00429 \textcolor{keywordtype}{short} si1,
+00430 \textcolor{keywordtype}{short} sj1,
+00431 \textcolor{keywordtype}{short} sp1,
+00432 \textcolor{keywordtype}{short} sq1));
+00433
+00437 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy}( \textcolor{keywordtype}{int} u,
+00438 \textcolor{keywordtype}{int} type,
+00439 \textcolor{keywordtype}{short} si1,
+00440 \textcolor{keywordtype}{short} sj1,
+00441 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}));
+00442
+00443 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff